R. intestinalis survives post-glucose (and post-mucin-degradation products) depletion by entering a slow-growth mode.
A combination of targeted metabolomics and RNA-seq showed that the slow growth mode of R. intestinalis represents a diauxic shift towards acetate and lactate consumption (both leading to butyrate production).
R. intestinalis consistently increased the expression of genes involved in glycolysis, pyruvate utilization, mucin hydrolysis, galactose and mannose utilization, and the butyrate-producing process after depletion of glucose/pyruvate.
Fermentation
RNA expression data
Annotation for expression dataset
Meta-data for fermentation dataset
Removing empty time-points from fermentation dataset
Subsetting RNA expression to wild type R. intestinalis only
ri_expression_data |>
pivot_longer(cols = -X,
names_to = "sample",
values_to = "expression") |>
inner_join(ri_metadata, by = c("sample" = "GC.code" )) |>
filter(Exp == "RI_batch_WC") |>
select(X,expression,sample) |>
pivot_wider(names_from = sample,
values_from = expression) |>
write_csv("../data/02_data_clean.csv")